Robert Schlegel

My name is rob and I love fish and kelp

Morgan Brand

• PhD student at the University of Cape Town
• @Morgs_John
• morganjbrand@gmail.com

The relevant not so distant past

The present and the future

1. Devise a fancy question and call it a hypothesis

2. Formulate a means of collecting the relevant data

3. Import data set into statistical software package

4. Run the procedure to get results

5. Copy and paste appropriate pieces from the analysis into document editor

6. Add descriptions

7. Finish/submit report for comments

   REPEAT steps 2 - 7 after receiving comments indefinately..

• The process of data capture is not open

• Lots of manual work (prone to make errors)

• Tedious (who likes to carefully copy-and-paste?)

• Likely not recordable (did you write down all the steps you followed to get your analysis?)

• What if you made an error at the beginning of your analysis? If your data had an error? If your hypothesis was biased?

• R is a free software package for statistical analysis and graphics.

• It excels in helping you with:
  • data manipulation
  • automation
  • reproducibility
  • improved accuracy
  • error finding
  • customizability
  • beautiful visualizations
  • Any downsides?

R is an older version that favours the command line programmer

RStudio is a powerful user interface that helps you get better control of your analysis.

• Like R, it is also completely free.

• You can write your entire paper/report (text, code, analysis, graphics, etc.) all in a language called R Markdown.

• If you need to update any of your code, R Markdown will automatically update your plots and output of your analysis and will create an updated PDF file.

• No more copy-and-paste!

• “Literate programming”

• Embed R code in a Markdown document

• Renders textual output along with graphics

Bookdown is one of the more recent additions to the R-universe.

Some highlights are:

• Multiple output formats

• Focus on writing the content not typesetting

• Readers can interact with examples

• Feedback and contributions as the book is developed

• Integrates with version control

Thesisdown is built from bookdown

The current output for the four versions is here:

• PDF
• Word
• ePub
• HTML and Gitbook

You can now increase your online voice using tools developed in your research methods and present them as a blog!

• The R package blogdown allows you to create websites using R Markdown

The website is generated from R Markdown documents

• all your results
• analysis
• graphics

can be computed and rendered dynamically from R code to your website!

Git is a version control system that lets you track changes to files over time

• Git manages the evolution of a set of files – called a repository

Github is a website for storing your git versioned files remotely

• Github provides a home for your Git-based projects on the internet

• If you are a student you can get the micro account which includes 5 private repositories for free!